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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ), 'gf_id' => 'HOM05D001262', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001262' ), 'data_identifier' => 'HOM05D001262', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001262', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '495', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p38440' => 'bna', 'A02p06010' => 'bna', 'A03p39420' => 'bna', 'A05p18850' => 'bna', 'A05p18990' => 'bna', 'A05p33770' => 'bna', 'A06p01680' => 'bna', 'A06p32330' => 'bna', 'A08p01950' => 'bna', 'Aa31LG10G2350' => 'aar', 'Aa31LG7G2770' => 'aar', 'Aa31LG8G2850' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1448' => 'aag', 'Actinidia08813' => 'ach', 'Actinidia13252' => 'ach', 'Actinidia16000' => 'ach', 'Actinidia22010' => 'ach', 'Actinidia22366' => 'ach', 'Actinidia40446' => 'ach', 'Ah.09g225650' => 'amhyb', 'Ah.10g026230' => 'amhyb', 'Ah.12g064000' => 'amhyb', 'AL1G54200' => 'aly', 'AL1G56470' => 'aly', 'AL1G60710' => 'aly', 'AL1G60980' => 'aly', 'AL1G60990' => 'aly', 'AL1G61000' => 'aly', 'AL1G61010' => 'aly', 'AL3G28310' => 'aly', 'AL3G41460' => 'aly', 'AL6G31610' => 'aly', 'Aqoxy7G02074' => 'aox', 'Aqoxy7G03751' => 'aox', 'arahy.Tifrunner.gnm1.ann1.407M44' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.86V3X8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ERFU6K' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IB1TIP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IIC4VI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.KX3KG5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NM15TM' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.S5HWQ6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZL0G7D' => 'arhy', 'AT1G47780' => 'ath', 'AT1G47786' => 'ath', 'AT1G51300' => 'ath', 'AT1G52440' => 'ath', 'AT1G52460' => 'ath', 'AT1G52470' => 'ath', 'AT1G52695' => 'ath', 'AT1G52700' => 'ath', 'AT3G15650' => 'ath', 'AT5G20060' => 'ath', 'ATR0815G019' => 'atr', 'Atru.chr1.3108' => 'acertr', 'Atru.chr1.3109' => 'acertr', 'Atru.chr7.1231' => 'acertr', 'Atru.chr7.2382' => 'acertr', 'AUR62011076' => 'cqu', 'AUR62011571' => 'cqu', 'AUR62016388' => 'cqu', 'AUR62018335' => 'cqu', 'AUR62024884' => 'cqu', 'AUR62026188' => 'cqu', 'AUR62029061' => 'cqu', 'AUR62030663' => 'cqu', 'AUR62033458' => 'cqu', 'AUR62042226' => 'cqu', 'AUR62043015' => 'cqu', 'BcaB01g04812' => 'bca', 'BcaB01g04813' => 'bca', 'BcaB02g10975' => 'bca', 'BcaB04g17146' => 'bca', 'BcaB04g20255' => 'bca', 'BcaB04g20910' => 'bca', 'BcaB05g22876' => 'bca', 'BcaC01g01335' => 'bca', 'BcaC01g02780' => 'bca', 'BcaC01g03864' => 'bca', 'BcaC03g13729' => 'bca', 'BcaC06g33327' => 'bca', 'BcaC08g43997' => 'bca', 'BcaC08g44010' => 'bca', 'BcaC09g48545' => 'bca', 'BcaC09g48546' => 'bca', 'BNapus_Darmor_BZH_scaffold_38p01830' => 'bna', 'BolC1t04830H' => 'bol', 'BolC2t07011H' => 'bol', 'BolC3t17059H' => 'bol', 'BolC3t18311H' => 'bol', 'BolC3t21402H' => 'bol', 'BolC5t33828H' => 'bol', 'BolC6t36580H' => 'bol', 'BolC6t36597H' => 'bol', 'BraA01t03894Z' => 'bra', 'BraA03t13092Z' => 'bra', 'BraA05t20781Z' => 'bra', 'BraA05t22200Z' => 'bra', 'BraA06t23386Z' => 'bra', 'BraA06t26159Z' => 'bra', 'BraA08t32247Z' => 'bra', 'C01p48750' => 'bna', 'C03p47800' => 'bna', 'C03p60510' => 'bna', 'C03p90840' => 'bna', 'C05p50780' => 'bna', 'C06p14030' => 'bna', 'C06p14220' => 'bna', 'C07p45990' => 'bna', 'CAN.G395.43' => 'can', 'CAN.G713.24' => 'can', 'CAN.G98.31' => 'can', 'CANSAT56G0458' => 'cansat', 'CANSAT56G2832' => 'cansat', 'CARHR042830' => 'chi', 'CARHR042840' => 'chi', 'CARHR090740' => 'chi', 'CARHR107260' => 'chi', 'CARHR179860' => 'chi', 'CARHR192770' => 'chi', 'Carub.0001s4143' => 'cru', 'Carub.0001s4144' => 'cru', 'Carub.0001s4170' => 'cru', 'Carub.0001s4171' => 'cru', 'Carub.0001s4172' => 'cru', 'Carub.0001s4173' => 'cru', 'Carub.0001s4174' => 'cru', 'Carub.0001s4176' => 'cru', 'Carub.0002s0914' => 'cru', 'Carub.0002s0920' => 'cru', 'Carub.0003s1540' => 'cru', 'Carub.0006s1844' => 'cru', 'Ca_01087_v3' => 'car', 'Ca_15723_v3' => 'car', 'Ca_27311_v3' => 'car', 'CBR_g44615' => 'cbr', 'Cc00_g31930' => 'ccan', 'Cc04_g03960' => 'ccan', 'Cc06_g08890' => 'ccan', 'Cc11_g01870' => 'ccan', 'Cc11_g01880' => 'ccan', 'CDE01G0286' => 'cde', 'CDE03G0268' => 'cde', 'Cfa002014' => 'cfa', 'Cfa003335' => 'cfa', 'Cfa013174' => 'cfa', 'Cfa025025' => 'cfa', 'Cfa025413' => 'cfa', 'Ciclev10009080m.g' => 'ccl', 'Ciclev10009255m.g' => 'ccl', 'Ciclev10026074m.g' => 'ccl', 'CiPaw.01G243800' => 'cil', 'CiPaw.02G154500' => 'cil', 'CiPaw.03G240400' => 'cil', 'CiPaw.04G169800' => 'cil', 'CiPaw.07G221100' => 'cil', 'CiPaw.08G013100' => 'cil', 'ClCG06G010850' => 'cla', 'ClCG07G012850' => 'cla', 'ClCG08G013150' => 'cla', 'COL.COLO4_12885' => 'col', 'COL.COLO4_23980' => 'col', 'COL.COLO4_35184' => 'col', 'Cpa.g.sc10.220' => 'cpa', 'Cpa.g.sc115.17' => 'cpa', 'Cpa.g.sc75.70' => 'cpa', 'Cpa.g.sc75.71' => 'cpa', 'Cre03.g164350' => 'cre', 'CsaV3_1G029760' => 'csa', 'CsaV3_2G031870' => 'csa', 'CsaV3_4G001340' => 'csa', 'CSS0001642' => 'camsi', 'CSS0002715' => 'camsi', 'CSS0003754' => 'camsi', 'CSS0004209' => 'camsi', 'CSS0011255' => 'camsi', 'CSS0016034' => 'camsi', 'CSS0016205' => 'camsi', 'CSS0025619' => 'camsi', 'CSS0028726' => 'camsi', 'CSS0031623' => 'camsi', 'CSS0037505' => 'camsi', 'CSS0041405' => 'camsi', 'CSS0048549' => 'camsi', 'DCAR_003042' => 'dca', 'DCAR_009207' => 'dca', 'DCAR_014862' => 'dca', 'DCAR_021327' => 'dca', 'DCAR_025481' => 'dca', 'Dinv11621' => 'din', 'Dinv30171' => 'din', 'Dinv30564' => 'din', 'Dinv30565' => 'din', 'Dinv36565' => 'din', 'Dinv38094' => 'din', 'Dinv41541' => 'din', 'Duzib150G0113' => 'dzi', 'Duzib168G0039' => 'dzi', 'Duzib168G0537' => 'dzi', 'Duzib168G1811' => 'dzi', 'Duzib187G0080' => 'dzi', 'Duzib187G1797' => 'dzi', 'Duzib235G0607' => 'dzi', 'ECA232G1741' => 'eca', 'ECA234G2925' => 'eca', 'ECA234G4366' => 'eca', 'ECA240G2187' => 'eca', 'ECA246G3329' => 'eca', 'ECA247G0621' => 'eca', 'EL10Ac1g01026' => 'bvu', 'EL10Ac2g02596' => 'bvu', 'EL10Ac8g18599' => 'bvu', 'EL10Ac9g21951' => 'bvu', 'Eucgr.C01119' => 'egr', 'Eucgr.F02550' => 'egr', 'Eucgr.J03039' => 'egr', 'FAN02G4112' => 'fan', 'FAN05G1538' => 'fan', 'FAN09G3099' => 'fan', 'FAN14G3513' => 'fan', 'FAN15G1043' => 'fan', 'FAN19G0437' => 'fan', 'FAN20G2523' => 'fan', 'FAN23G1170' => 'fan', 'FAN24G2862' => 'fan', 'FAN26G2167' => 'fan', 'FAN27G1991' => 'fan', 'FAN28G0750' => 'fan', 'FvH4_1g03850' => 'fve', 'FvH4_2g29580' => 'fve', 'FvH4_6g30430' => 'fve', 'Glyma.04G068500' => 'gma', 'Glyma.04G149900' => 'gma', 'Glyma.06G070100' => 'gma', 'Glyma.06G215700' => 'gma', 'Glyma.06G215900' => 'gma', 'Glyma.07G032700' => 'gma', 'Glyma.08G209800' => 'gma', 'Glyma.13G363000' => 'gma', 'Glyma.15G010800' => 'gma', 'Gohir.A05G018800' => 'ghi', 'Gohir.A05G124700' => 'ghi', 'Gohir.A06G057550' => 'ghi', 'Gohir.A06G057600' => 'ghi', 'Gohir.A06G187100' => 'ghi', 'Gohir.A09G112675' => 'ghi', 'Gohir.A10G076600' => 'ghi', 'Gohir.A13G198800' => 'ghi', 'Gohir.D05G019900' => 'ghi', 'Gohir.D05G125700' => 'ghi', 'Gohir.D06G055900' => 'ghi', 'Gohir.D06G193300' => 'ghi', 'Gohir.D10G074700' => 'ghi', 'Gohir.D13G204200' => 'ghi', 'Gorai.009G020100' => 'gra', 'Gorai.009G129700' => 'gra', 'Gorai.010G065200' => 'gra', 'Gorai.010G065500' => 'gra', 'Gorai.010G227200' => 'gra', 'Gorai.011G080600' => 'gra', 'Gorai.013G233000' => 'gra', 'GSVIVG01015490001' => 'vvi', 'GSVIVG01017241001' => 'vvi', 'GSVIVG01035817001' => 'vvi', 'HanXRQChr00c0540g0575641' => 'han', 'HanXRQChr02g0032511' => 'han', 'HanXRQChr02g0050801' => 'han', 'HanXRQChr04g0096731' => 'han', 'HanXRQChr04g0097201' => 'han', 'HanXRQChr06g0180221' => 'han', 'HanXRQChr09g0274901' => 'han', 'HanXRQChr10g0303861' => 'han', 'HanXRQChr13g0402721' => 'han', 'HanXRQChr16g0500571' => 'han', 'HanXRQChr16g0501371' => 'han', 'Haze_16507' => 'cav', 'Haze_21559' => 'cav', 'Haze_25629' => 'cav', 'Hma1.2p1_0000F.1_g000640' => 'hma', 'Hma1.2p1_0018F.1_g012760' => 'hma', 'HPP92_009842' => 'vpl', 'Hund00553' => 'sun', 'Hund03021' => 'sun', 'Hund06584' => 'sun', 'Hund09152' => 'sun', 'Hund26471' => 'sun', 'Lalb_Chr08g0234851' => 'lal', 'Lalb_Chr08g0243971' => 'lal', 'Lalb_Chr11g0063841' => 'lal', 'Lalb_Chr14g0373661' => 'lal', 'Lalb_Chr23g0275281' => 'lal', 'Lalb_Chr24g0395621' => 'lal', 'Lalb_Chr25g0279511' => 'lal', 'Lalb_Chr25g0279521' => 'lal', 'Lj1g0018853' => 'lja', 'Lj1g0023618' => 'lja', 'Lj3g0016654' => 'lja', 'Lj3g0022336' => 'lja', 'Lj5C68T14' => 'lonja', 'Lj7A633T40' => 'lonja', 'Lj8C624T9' => 'lonja', 'Lj9C502G2' => 'lonja', 'Lsat_1_v5_gn_1_33581' => 'lsa', 'Lsat_1_v5_gn_4_106341' => 'lsa', 'Lsat_1_v5_gn_5_31640' => 'lsa', 'Lsat_1_v5_gn_5_92300' => 'lsa', 'Lsat_1_v5_gn_5_98900' => 'lsa', 'Lsat_1_v5_gn_6_22260' => 'lsa', 'Lsat_1_v5_gn_7_42521' => 'lsa', 'Lsat_1_v5_gn_8_57300' => 'lsa', 'Manes.03G017200' => 'mes', 'Manes.04G117300' => 'mes', 'Manes.06G053100' => 'mes', 'Manes.11G052300' => 'mes', 'Manes.14G129428' => 'mes', 'MBI01_g11881_MAGBIO' => 'mbi', 'MBI04_g10414_MAGBIO' => 'mbi', 'MCO05G361' => 'mco', 'MCO11G308' => 'mco', 'MD02G1036900' => 'mdo', 'MD08G1145500' => 'mdo', 'MD09G1221600' => 'mdo', 'MD15G1121100' => 'mdo', 'MD15G1177000' => 'mdo', 'MD17G1203800' => 'mdo', 'Medtr2g054780' => 'mtr', 'Medtr2g103140' => 'mtr', 'Medtr3g107630' => 'mtr', 'Medtr4g011320' => 'mtr', 'MELO3C011237.2' => 'cme', 'MELO3C017906.2' => 'cme', 'MELO3C026638.2' => 'cme', 'MELO3C029577.2' => 'cme', 'Migut.E01472' => 'egut', 'Migut.I00804' => 'egut', 'Migut.O00076' => 'egut', 'MSTRG.11114' => 'ama', 'MSTRG.11774' => 'ama', 'MSTRG.1636' => 'ama', 'MSTRG.22724' => 'ama', 'Nitab4.5_0000151g0120' => 'nta', 'Nitab4.5_0000620g0100' => 'nta', 'Nitab4.5_0001672g0060' => 'nta', 'Nitab4.5_0003011g0010' => 'nta', 'Nitab4.5_0003512g0040' => 'nta', 'Nitab4.5_0003722g0010' => 'nta', 'Nitab4.5_0004789g0010' => 'nta', 'Nitab4.5_0005275g0060' => 'nta', 'Nn2g11941' => 'nnu', 'Nn6g34041' => 'nnu', 'Nn8g39373' => 'nnu', 'Oeu018455.2' => 'oeu', 'Oeu021593.1' => 'oeu', 'Oeu030206.1' => 'oeu', 'Oeu033462.1' => 'oeu', 'Oeu052289.1' => 'oeu', 'Oeu063815.1' => 'oeu', 'Oeu063818.1' => 'oeu', 'Os01g0175000' => 'osa', 'Os01g0612500' => 'osa', 'Os04g0174900' => 'osa', 'Os05g0588100' => 'osa', 'Peaxi162Scf00015g00440' => 'pax', 'Peaxi162Scf00034g01310' => 'pax', 'Peaxi162Scf00207g00737' => 'pax', 'Peaxi162Scf00341g00015' => 'pax', 'Peaxi162Scf00546g00534' => 'pax', 'PGR031G0110' => 'pgr', 'PGR102G2686' => 'pgr', 'PGR142G2359' => 'pgr', 'PGSC0003DMG400028544' => 'stu', 'PGSC0003DMG400028622' => 'stu', 'PGSC0003DMG400033649' => 'stu', 'Phvul.005G174700' => 'pvu', 'Phvul.009G095000' => 'pvu', 'Phvul.009G198700' => 'pvu', 'Phvul.010G153400' => 'pvu', 'Potri.001G173700' => 'ptr', 'Potri.003G060300' => 'ptr', 'Potri.006G251100' => 'ptr', 'Potri.018G030200' => 'ptr', 'Potri.018G070700' => 'ptr', 'Pp3c12_16460' => 'ppa', 'Pp3c21_6410' => 'ppa', 'Prupe.1G473700' => 'ppe', 'Prupe.3G078700' => 'ppe', 'Prupe.7G238500' => 'ppe', 'Psat0ss3186g0320' => 'psa', 'Psat1g026760' => 'psa', 'Psat5g300520' => 'psa', 'Psat7g255120' => 'psa', 'PSO170G3226' => 'pso', 'PSO210G1247' => 'pso', 'PSO210G3662' => 'pso', 'PSO210G4920' => 'pso', 'PSO210G5233' => 'pso', 'PSO339G3506' => 'pso', 'PSO384G0068' => 'pso', 'PSO455G0091' => 'pso', 'QL02p022448' => 'qlo', 'QL02p087480' => 'qlo', 'QL05p027571' => 'qlo', 'RcHm_v2.0_Chr2g0089241' => 'rch', 'RcHm_v2.0_Chr2g0136771' => 'rch', 'RcHm_v2.0_Chr4g0431191' => 'rch', 'RcHm_v2.0_Chr6g0298561' => 'rch', 'Rhsim01G0077600' => 'rsi', 'Rhsim07G0148200' => 'rsi', 'Rhsim08G0216700' => 'rsi', 'Rhsim12G0193600' => 'rsi', 'Sabra01G0138100' => 'sbr', 'Sabra03G0034600' => 'sbr', 'Sabra18G0031900' => 'sbr', 'Sabra18G0061800' => 'sbr', 'SalBow2G1720' => 'sbo', 'SalBow2G2691' => 'sbo', 'SalBow4G1356' => 'sbo', 'SalBow6G6322' => 'sbo', 'Sc08g0006820' => 'sci', 'Sc10g0005580' => 'sci', 'Sc18g0000800' => 'sci', 'Sc23g0006900' => 'sci', 'Sed0003376' => 'sed', 'Sed0005386' => 'sed', 'Sed0005651' => 'sed', 'Sed0011913' => 'sed', 'Sed0014878' => 'sed', 'Sed0015148' => 'sed', 'Sed0024054' => 'sed', 'SEGI_05105' => 'sgi', 'SEGI_16479' => 'sgi', 'SEGI_25548' => 'sgi', 'SGA_v2.0_scaffold22G09930' => 'sas', 'SGA_v2.0_scaffold37G14788' => 'sas', 'SMO347G0182' => 'smo', 'Solyc06g067950.3' => 'sly', 'Solyc08g067160.3' => 'sly', 'Solyc12g006870.2' => 'sly', 'Solyc12g042890.2' => 'sly', 'Sopen06g025230' => 'spe', 'Sopen08g021100' => 'spe', 'Sopen12g002840' => 'spe', 'Sopen12g022050' => 'spe', 'Sp1g39240' => 'spa', 'Sp1g39250' => 'spa', 'Sp1g39260' => 'spa', 'Sp1g39270' => 'spa', 'Sp3g13950' => 'spa', 'Sp6g24350' => 'spa', 'TAR383G0219' => 'tar', 'TAR625G1143' => 'tar', 'TAR626G0257' => 'tar', 'TAR636G1807' => 'tar', 'TAR636G2536' => 'tar', 'THA.LOC104799650' => 'tha', 'THA.LOC104811039' => 'tha', 'THA.LOC104818038' => 'tha', 'Thecc.06G074300' => 'tca', 'Thecc.09G121300' => 'tca', 'Thecc.09G149400' => 'tca', 'Thhalv10011726m.g' => 'esa', 'Thhalv10011946m.g' => 'esa', 'Thhalv10011963m.g' => 'esa', 'Thhalv10012079m.g' => 'esa', 'Thhalv10012083m.g' => 'esa', 'Thhalv10012094m.g' => 'esa', 'Thhalv10012118m.g' => 'esa', 'Thhalv10012252m.g' => 'esa', 'Thhalv10014480m.g' => 'esa', 'Thhalv10021374m.g' => 'esa', 'TPR.G15009' => 'tpr', 'TPR.G1701' => 'tpr', 'TPR.G31758' => 'tpr', 'TWI12G0346' => 'twi', 'TWI32G0977' => 'twi', 'TWI34G0221' => 'twi', 'TWI34G0483' => 'twi', 'TWI63G1680' => 'twi', 'TWI75G0422' => 'twi', 'unitig_27.g25339' => 'ugi', 'unitig_61.g26248' => 'ugi', 'unitig_744.g24454' => 'ugi', 'vmacro05193' => 'vma', 'vmacro16920' => 'vma', 'vmacro20654' => 'vma', 'VMungo0331G1421' => 'vmu', 'VMungo1080G0213' => 'vmu', 'VMungo1309G0794' => 'vmu', 'VMungo1309G2166' => 'vmu', 'VMungo1309G2178' => 'vmu', 'VMungo1309G3035' => 'vmu', 'Zm00001eb122690' => 'zma', 'Zm00001eb161910' => 'zma', 'Zm00001eb336850' => 'zma', 'Zm00001eb345070' => 'zma' ) $gf_id = 'HOM05D001262' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001262' ) $data_identifier = 'HOM05D001262' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 18, 'aar' => (int) 3, 'aag' => (int) 1, 'ach' => (int) 6, 'amhyb' => (int) 3, 'aly' => (int) 10, 'aox' => (int) 2, 'arhy' => (int) 9, 'ath' => (int) 10, 'atr' => (int) 1, 'acertr' => (int) 4, 'cqu' => (int) 11, 'bca' => (int) 16, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 3, 'cansat' => (int) 2, 'chi' => (int) 6, 'cru' => (int) 12, 'car' => (int) 3, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 2, 'cfa' => (int) 5, 'ccl' => (int) 3, 'cil' => (int) 6, 'cla' => (int) 3, 'col' => (int) 3, 'cpa' => (int) 4, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 13, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 4, 'egr' => (int) 3, 'fan' => (int) 12, 'fve' => (int) 3, 'gma' => (int) 9, 'ghi' => (int) 14, 'gra' => (int) 7, 'vvi' => (int) 3, 'han' => (int) 11, 'cav' => (int) 3, 'hma' => (int) 2, 'vpl' => (int) 1, 'sun' => (int) 5, 'lal' => (int) 8, 'lja' => (int) 4, 'lonja' => (int) 4, 'lsa' => (int) 8, 'mes' => (int) 5, 'mbi' => (int) 2, 'mco' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 4, 'cme' => (int) 4, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 8, 'nnu' => (int) 3, 'oeu' => (int) 7, 'osa' => (int) 4, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 4, 'ptr' => (int) 5, 'ppa' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 4, 'pso' => (int) 8, 'qlo' => (int) 3, 'rch' => (int) 4, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 4, 'sci' => (int) 4, 'sed' => (int) 7, 'sgi' => (int) 3, 'sas' => (int) 2, 'smo' => (int) 1, 'sly' => (int) 4, 'spe' => (int) 4, 'spa' => (int) 6, 'tar' => (int) 5, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 10, 'tpr' => (int) 3, 'twi' => (int) 6, 'ugi' => (int) 3, 'vma' => (int) 3, 'vmu' => (int) 6, 'zma' => (int) 4 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb345070' $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